raklet wrote:I checked my local MLS and the report was there. It appears that entering it online will sync it with the Ward level MLS but not the Stake.

Quarterly report data does indeed sync to stake MLS. I'm a stake clerk, and I see reports from all our wards in MLS. Some of our wards enter report data in MLS, and some on LDS.org. The obvious question for your stake clerk would be if he did a Send/Receive before generating the report in stake MLS.